DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.
BMC Genomics
; 11: 244, 2010 Apr 16.
Article
em En
| MEDLINE
| ID: mdl-20398377
ABSTRACT
BACKGROUND:
DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number.RESULTS:
We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual.CONCLUSION:
The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Tumor Carcinoide
/
Telômero
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Variações do Número de Cópias de DNA
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Neoplasias Pulmonares
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Mitocôndrias
Limite:
Animals
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Female
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Humans
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Male
Idioma:
En
Ano de publicação:
2010
Tipo de documento:
Article